RetrogeneDB ID: retro_ptro_975

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:59964291..59964821(-)
• Located in intron of: ENSPTRG00000006412

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSPTRG00000000138
• Aliases: None
• Description: None

Sequence

>retro_ptro_975
TTCTGCAAGACATGCAGTCTGTGGCCCACCCATGCCTTGTCACTGCAGGTGGAGCAGCTGCCCCCCACCAGTGCTCACAG
TACTAGGATACCTTTGTCATCTGCAGTAAGACCTATGGCAACATGATGGCGTTGGATGGCATCATCCAGTATACAGAGAG
GAACAAGTTCTCCTACCAGGAGATTATAGTCAACCTGCCTCTCTGCAGCCACCCCAACCTACAAAATGGTGGTGATTATT
GAGGACAGGAACGAGGGCATCCTGTGCAAGGTGAGGTAGTACCCCTCTGTGAAGTCTATGGTCCAATGTGAGACTGATAA
GGATGTCATCCAAGTCTCTCAGAAGTTCCTGCCAGGCAAAGCTGTTGGCTACTTTTGCTCAAAGCTGACCTTACACATGG
GTGATGGGTTTGAATTCATGAAACAGAATTAGGATGCCTTCAGTGTTATCAATGACTCCTCAGACCCCACTGCCTTGCTA
AAAACCTCTTCAAGGAATCCTACTACCAGCTCATGAAGACAGTCCTCAGG

Alignment

ORF - retro_ptro_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 58.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FRETCSLWPGQALSLQVEQL-LHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLC
          F..TCSLWP..ALSLQVEQL...H..S.Y.D..V..SKTYGN...LDG.IQ.TER..FSYQE.I.NLPLC
Retrocopy FCKTCSLWPTHALSLQVEQL<APHQCSQY*DTFVICSKTYGNMMALDGIIQYTERNKFSYQEIIVNLPLC

Parental  SHPNPRK-VLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFE
          SHPN....V.II.....G.L..V...PSV.S.VQCE.D.DVIQVS.KFLPG.A.GY..SKLTLH.GDGFE
Retrocopy SHPNLQN>VVIIEDRNEGILCKVR*YPSVKSMVQCETDKDVIQVSQKFLPGKAVGYFCSKLTLHMGDGFE

Parental  FMKQNQDAFDVIITDSSDPMG-PAESLFKESYYQLMKTALK
          FMKQN.DAF.V.I.DSSDP....A..LFKESYYQLMKT.L.
Retrocopy FMKQN*DAFSV-INDSSDPTA<LAKNLFKESYYQLMKTVLR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.09 RPM	54.73 RPM
SRP007412_cerebellum	0.11 RPM	29.18 RPM
SRP007412_heart	0.09 RPM	14.81 RPM
SRP007412_kidney	0.05 RPM	22.28 RPM
SRP007412_liver	0.03 RPM	38.66 RPM
SRP007412_testis	0.00 RPM	11.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_975 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_975 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1426
Macaca mulatta	retro_mmul_2259

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688, retro_ptro_975 ,